Contacts of the strand formed by residues 506 - 509 (chain A) in PDB entry 1H7B


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with SER 506 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    476A  PHE*     3.7     1.2    -      -       -      -
    477A  HIS*     4.5     1.8    -      -       -      -
    490A  ILE*     5.7     2.5    -      -       -      -
    493A  GLU*     2.6    35.0    +      -       -      +
    497A  HIS*     2.8    25.2    +      -       -      -
    505A  ILE*     1.3    77.8    +      -       -      +
    507A  TYR*     1.3    65.4    +      -       -      +
    531A  LEU*     3.8    17.1    -      -       -      +
    533A  TYR      3.3     4.2    +      -       -      -
    534A  PHE*     3.2    14.3    -      -       -      -
    535A  GLY      3.1    24.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 507 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233A  LYS*     5.1     1.7    +      -       -      -
    268A  ASP*     5.4     0.2    +      -       -      -
    291A  ARG*     3.1    25.5    +      -       -      -
    477A  HIS*     3.9    23.8    -      +       +      +
    489A  LYS*     3.2    31.7    +      -       -      +
    493A  GLU*     4.2     2.5    +      -       -      +
    505A  ILE*     3.8    32.1    -      -       +      +
    506A  SER*     1.3    77.6    -      -       -      +
    508A  VAL*     1.3    66.1    +      -       -      +
    534A  PHE*     4.4     0.4    -      -       -      -
    535A  GLY*     3.3    15.9    -      -       -      -
    537A  ASN*     3.6    29.8    -      -       -      +
    577A  ARG*     3.4    28.7    +      -       -      -
    579A  CYS      3.4    21.3    -      -       -      -
    580A  ALA      3.6    13.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 508 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    486A  PRO*     3.8    38.8    -      -       +      +
    489A  LYS*     4.1    13.0    -      -       +      +
    490A  ILE*     4.0     7.2    -      -       +      +
    507A  TYR*     1.3    79.2    -      -       -      +
    509A  GLU*     1.3    65.0    +      -       -      +
    510A  LEU*     3.3    35.2    +      -       +      -
    523A  VAL*     4.4     4.7    -      -       +      -
    534A  PHE*     3.9    25.4    -      -       +      -
    535A  GLY      3.5     5.2    +      -       -      +
    536A  VAL*     3.8     3.0    -      -       +      +
    537A  ASN*     2.9    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 509 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    480A  VAL*     5.5     8.2    -      -       +      +
    486A  PRO*     4.6     3.6    -      -       -      +
    489A  LYS*     5.1     8.0    -      -       -      +
    508A  VAL*     1.3    78.3    -      -       -      +
    510A  LEU*     1.3    71.6    +      -       -      +
    537A  ASN*     3.3    36.4    +      -       -      +
    577A  ARG      4.5     3.8    -      -       -      +
    578A  THR*     5.5     3.5    -      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il